Secondly, I do not have a group (control Vs treated). I would like to identify differentially expressed genes in a particular individual compared with a mean of all the individuals (Intercept). I would like to repeat it for all the individuals.

I think that the current wording is confusing. The explanation states "This ensures that a gene will be retained if it is expressed in both the libraries belonging to any of the six groups.". I read this as the two samples will belong to the same class, whereas the filtering is independent of samples' classes and the two samples with sufficient reads could belong to two different classes.

The form of the quoted sentence is "if A then B", but you are reading it to mean "if B then A".

You're not the first person to make the same interpretation, so I guess that making the reasoning longer and even more explicit may have been worthwhile. I'm always surprised by how much confusion the issue of filtering causes. However we are not planning to make changes to this published article. Making changes would require the whole article to be re-refereed.